MODA for Calculations of Binding Free Energies and Potentials of Mean Force

Simulated in project SMARTNANOTOX

1. General physics of the model equations:
   1. Model type and name:
      Molecular dynamics with self-adjusted bias (Metadynamics)
   2. Model entity:
      Atoms
   3. Model physics / chemictry equations PE’s:
      1. Equations:
         pe_type_atomistic_molecular_dynamics
         Newtons equation of motion
         V-rescale thermostat
         Bias potential for the surface separation distance, which is determined according to the well-tempered metadynamics equations
         The PMF is computed by integration of the average force acting on the solvent at the given distance from the surface
         
      2. Physical quantities for each equation:
         atoms coordinates; atom velocities; biased potential
   1. Materials relations:
      1. MR equations:
         Material is described by a user-specified force field
         Biomolecules are described by the GAFF
         Water is described by the TIP3P model
      2. Physical quantities / descriptors for each MR:
         atoms coordinates; atom velocities; biased potential
   2. Simulation input:
      N/A
   3. Publication:
      G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi. PLUMED2: New feathers for an old bird, Comp. Phys. Comm. 185, 604 (2014), [doi:xxx]

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